I am trying to analyze immunofluorescence images from a 96-well plate using Qupath. I started with a czi file with multiple tile regions and used ZEN to export each tile region to an individual single-plane, 3-channel OME-TIFF.
When I open these files in ImageJ using the Bio-Formats importer with the Hyperstack setting (which defaults to XYCZT stack order), the image opens as expected, with three channels registered. However, when I try to import into Qupath using either the default or Bio-Formats image provider, the images are imported as a 3-slice z-stack with one channel (the little slider shows up in the upper-left corner). I assume this is because Qupath has used an XYZCT order.
Is there any way to either specify the proper order at the time of import in Qupath or to change the channel vs. slice structure of an image after it has been imported?